Spectroscopy, molecular vibrational

Vibrational spectroscopy provides detailed infonnation on both structure and dynamics of molecular species. Infrared (IR) and Raman spectroscopy are the most connnonly used methods, and will be covered in detail in this chapter. There exist other methods to obtain vibrational spectra, but those are somewhat more specialized and used less often. They are discussed in other chapters, and include inelastic neutron scattering (INS), helium atom scattering, electron energy loss spectroscopy (EELS), photoelectron spectroscopy, among others. 

Molecular clusters are weakly bound aggregates of stable molecules. Such clusters can be produced easily using supersonic expansion, and have been extensively studied by both electronic and vibrational spectroscopy [146,... 

Wilson, E. B. Jr, Decius, J. C. and Cross, P. C. (1980) Molecular Vibrations, Dover, New York. Woodward, L. A. (1972) Introduction to the Theory of Molecular Vibrations and Vibrational Spectroscopy, Oxford University Press, Oxford. 

In the chapter on vibrational spectroscopy (Chapter 6) 1 have expanded the discussions of inversion, ring-puckering and torsional vibrations, including some model potential functions. These types of vibration are very important in the determination of molecular structure. 

Analysis of Surface Molecular Composition. Information about the molecular composition of the surface or interface may also be of interest. A variety of methods for elucidating the nature of the molecules that exist on a surface or within an interface exist. Techniques based on vibrational spectroscopy of molecules are the most common and include the electron-based method of high resolution electron energy loss spectroscopy (hreels), and the optical methods of ftir and Raman spectroscopy. These tools are tremendously powerful methods of analysis because not only does a molecule possess vibrational modes which are signatures of that molecule, but the energies of molecular vibrations are extremely sensitive to the chemical environment in which a molecule is found. Thus, these methods direcdy provide information about the chemistry of the surface or interface through the vibrations of molecules contained on the surface or within the interface. 

Most informative in this context is vibrational spectroscopy since the number of signals observed depends on the molecular size as well as on the symmetry of the molecule and, if it is part of a condensed phase, of its environment. In particular, Raman spectroscopy has contributed much to the elucidation of the various allotropes of elemental sulfur and to the analysis of complex mixtures such as hquid and gaseous sulfur. 

Since the vibrational spectra of sulfur allotropes are characteristic for their molecular and crystalline structure, vibrational spectroscopy has become a valuable tool in structural studies besides X-ray diffraction techniques. In particular, Raman spectroscopy on sulfur samples at high pressures is much easier to perform than IR spectroscopical studies due to technical demands (e.g., throughput of the IR beam, spectral range in the far-infrared). On the other hand, application of laser radiation for exciting the Raman spectrum may cause photo-induced structural changes. High-pressure phase transitions and structures of elemental sulfur at high pressures were already discussed in [1]. 

Vibrational spectroscopy and in particular Raman spectroscopy is by far the most useful spectroscopic technique to qualitatively characterize polysulfide samples. The fundamental vibrations of the polysulfide dianions with between 4 and 8 atoms have been calculated by Steudel and Schuster [96] using force constants derived partly from the vibrational spectra of NayS4 and (NH4)2Ss and partly from cydo-Sg. It turned out that not only species of differing molecular size but also rotational isomers like Ss of either Cy or Cs symmetry can be recognized from pronounced differences in their spectra. The latter two anions are present, for instance, in NaySg (Cs) and KySg (Cy), respectively (see Table 2). 

The vibrations of molecular bonds provide insight into bonding and stmcture. This information can be obtained by infrared spectroscopy (IRS), laser Raman spectroscopy, or electron energy loss spectroscopy (EELS). IRS and EELS have provided a wealth of data about the stmcture of catalysts and the bonding of adsorbates. IRS has also been used under reaction conditions to follow the dynamics of adsorbed reactants, intermediates, and products. Raman spectroscopy has provided exciting information about the precursors involved in the synthesis of catalysts and the stmcture of adsorbates present on catalyst and electrode surfaces. 

Normal vibrational spectroscopy generates information about the molecular frequency of vibration, the intensity of the spectral line and the shape of the associated band. The first of these is related to the strength of the molecular bonds and is the main concern of this section. The intensity of the band is related to the degree to which the polarisability is modulated during the vibration and the band shape provides information about molecular reorientational motion. 

One of the most common uses of vibrational spectroscopy is as a molecular fingerprinting tool whereby spectral features are assigned to the presence of particular fragments in molecules. These assignments are, however, only... 

The use of computer simulations to study internal motions and thermodynamic properties is receiving increased attention. One important use of the method is to provide a more fundamental understanding of the molecular information contained in various kinds of experiments on these complex systems. In the first part of this paper we review recent work in our laboratory concerned with the use of computer simulations for the interpretation of experimental probes of molecular structure and dynamics of proteins and nucleic acids. The interplay between computer simulations and three experimental techniques is emphasized (1) nuclear magnetic resonance relaxation spectroscopy, (2) refinement of macro-molecular x-ray structures, and (3) vibrational spectroscopy. The treatment of solvent effects in biopolymer simulations is a difficult problem. It is not possible to study systematically the effect of solvent conditions, e.g. added salt concentration, on biopolymer properties by means of simulations alone. In the last part of the paper we review a more analytical approach we have developed to study polyelectrolyte properties of solvated biopolymers. The results are compared with computer simulations. 

Vibrational spectroscopy has played a very important role in the development of potential functions for molecular mechanics studies of proteins. Force constants which appear in the energy expressions are heavily parameterized from infrared and Raman studies of small model compounds. One approach to the interpretation of vibrational spectra for biopolymers has been a harmonic analysis whereby spectra are fit by geometry and/or force constant changes. There are a number of reasons for developing other approaches. The consistent force field (CFF) type potentials used in computer simulations are meant to model the motions of the atoms over a large ranee of conformations and, implicitly temperatures, without reparameterization. It is also desirable to develop a formalism for interpreting vibrational spectra which takes into account the variation in the conformations of the chromophore and surroundings which occur due to thermal motions. 

To emphasize the Important role played by vibrational spectroscopy In developing our understanding of molecular processes on surfaces, recent results for CO adsorption on clean and the sulfided Nl(lOO) surface (2) will be described. These vibrational results for CO adsorption on sulfided Nl(lOO) Indicate that CO-S... 

J. Phys. Chem. B, 106, 5143-5154. Somorjai, G. A. and Rupprechter, G. (1999) Molecular studies of catalytic reactions on crystal surfaces at high pressures and high temperatures by infrared-visible sum frequency generation (SFG) surface vibrational spectroscopy. J. Phys. Chem., 103, 1623-1638. 

Low-frequency vibrations of molecular submonolayers detected by time-domain raman spectroscopy. /. Mol. Struct., 735-736, 169-177. 

Guyot-Sionnest P, Hunt JH, Shen YR. 1987. Sum-fiequency vibrational spectroscopy of a Langmuir film Study of molecular orientation of a two-dimensional system. Phys Rev Lett 59 1597-1600. 

Vibrational spectroscopy provides the most definitive means of identifying the surface species arising from molecular adsorption and the species generated by surface reaction, and the two techniques that are routinely used for vibrational studies of molecules on surfaces are Infrared (IR) Spectroscopy and Electron Energy Loss Spectroscopy (HREELS) (q.v.). 

One of the classic examples of an area in which vibrational spectroscopy has contributed to the understanding of the surface chemistry of an adsorbate is that of the molecular adsorption of CO on metallic surfaces. Adsorbed CO usually gives rise to strong absorptions in both the IR and HREELS spectra at the (C-O) stretching frequency. The metal-carbon stretching mode ( 400 cm-1) is usually also accessible to HREELS. 

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